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- PDB-4o4b: Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA ... -

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Basic information

Entry
Database: PDB / ID: 4o4b
TitleCrystal Structure of an Inositol hexakisphosphate kinase EhIP6KA as a fusion protein with maltose binding protein
Components
  • Extracellular solute-binding protein family 1
  • Inositol hexakisphosphate kinase
KeywordsTRANSPORT PROTEIN/Transferase / PDKG kinase / TRANSPORT PROTEIN-Transferase complex
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / phosphatidylinositol phosphate biosynthetic process / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Entamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, H. / Shears, S.B.
CitationJournal: Nat Commun / Year: 2014
Title: IP6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family.
Authors: Wang, H. / DeRose, E.F. / London, R.E. / Shears, S.B.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 1
B: Inositol hexakisphosphate kinase


Theoretical massNumber of molelcules
Total (without water)73,1352
Polymers73,1352
Non-polymers00
Water11,782654
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.626, 51.980, 117.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Extracellular solute-binding protein family 1 / Maltose-binding periplasmic protein


Mass: 43451.062 Da / Num. of mol.: 1 / Fragment: UNP residues 27-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: malE, EcDH1_3962, ECDH1ME8569_3890 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3) / References: UniProt: C9QV44
#2: Protein Inositol hexakisphosphate kinase


Mass: 29683.938 Da / Num. of mol.: 1 / Fragment: UNP residues 32-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI7A_103520 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3)
References: UniProt: N9UNA8, inositol-hexakisphosphate 5-kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% (w/v) PEG 3350, 50 mM NaH2PO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 67725 / Num. obs: 67725 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.057 / Net I/σ(I): 39.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3301 / Rsym value: 0.457 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1EZ9 AND 1W2C

1ez9

1w2c


Resolution: 1.8→36.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.902 / SU ML: 0.087 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22102 3383 5 %RANDOM
Rwork0.19618 ---
all0.19744 64104 --
obs0.19744 64104 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2---0.19 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 0 654 5636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.025131
X-RAY DIFFRACTIONr_bond_other_d0.0050.024846
X-RAY DIFFRACTIONr_angle_refined_deg1.11.9646940
X-RAY DIFFRACTIONr_angle_other_deg0.74311228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36125.212236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18115915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4131516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8351.6062514
X-RAY DIFFRACTIONr_mcbond_other0.8351.6052513
X-RAY DIFFRACTIONr_mcangle_it1.4862.4023146
X-RAY DIFFRACTIONr_mcangle_other1.4862.4033147
X-RAY DIFFRACTIONr_scbond_it0.8441.7232617
X-RAY DIFFRACTIONr_scbond_other0.8441.7242618
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.422.5333795
X-RAY DIFFRACTIONr_long_range_B_refined9.27115.836601
X-RAY DIFFRACTIONr_long_range_B_other9.15613.9996222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 238 -
Rwork0.277 4390 -
obs--92.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3977-0.6082-0.6390.70620.21420.3387-0.0255-0.19850.09510.00840.087-0.06080.033-0.0033-0.06150.1557-0.0214-0.00830.3096-0.04750.1595-2.814.59375.2665
21.40910.31710.33561.3410.12941.2675-0.03620.0450.0279-0.0802-0.01240.0704-0.0947-0.05530.04870.09870-0.00760.02010.00460.084535.28981.32326.5383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 374
2X-RAY DIFFRACTION2B21 - 270

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